5
Evaluating Mississippi River Water Quality

Accurate evaluation of Mississippi River quality, and how that water quality changes over time, is important for several reasons. This information is essential in measuring the effectiveness of water quality remediation strategies such as Total Maximum Daily Loads (TMDLs). It also is central to determining if water quality standards are being met. More generally, knowledge of water quality in a river or a watershed often is of great interest to citizens, elected officials, and decision makers. Comprehensive and accurate portrayal of water quality conditions requires both the collection of data (monitoring) and an understanding of the system that is supported by scientific investigations (research). Ideally there will be clear and mutually supportive links between monitoring and research. Effective data gathering efforts also require a sustained commitment over time if water quality trends are to be detected and evaluated.

Monitoring and evaluating Mississippi River water quality poses unique challenges because (1) monitoring efforts face logistical difficulties and hazards in some parts of the river system; (2) processes and natural fluctuations in the Mississippi River operate on scales of decades and over hundreds of miles; (3) the river spans, or forms, boundaries of political units or jurisdictions that have differing priorities and resources; and (4) water quality standards and environmental conditions vary across the entire system. For example, because of natural, longitudinal changes in water quality from upstream to downstream, levels of suspended sediment and turbidity that would be considered “pristine” (i.e., pre-settlement) in the lower reaches of the Mississippi River would be considered objectionable and indicative of severe degradation if encountered in the river’s headwaters. Likewise, because of natural patterns and differences along the river’s length, water

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5
Evaluating Mississippi
River Water Quality
A
ccurate evaluation of Mississippi River quality, and how that water
quality changes over time, is important for several reasons. This
information is essential in measuring the effectiveness of water qual-
ity remediation strategies such as Total Maximum Daily Loads (TMDLs).
It also is central to determining if water quality standards are being met.
More generally, knowledge of water quality in a river or a watershed often
is of great interest to citizens, elected officials, and decision makers. Com-
prehensive and accurate portrayal of water quality conditions requires both
the collection of data (monitoring) and an understanding of the system that
is supported by scientific investigations (research). Ideally there will be clear
and mutually supportive links between monitoring and research. Effective
data gathering efforts also require a sustained commitment over time if
water quality trends are to be detected and evaluated.
Monitoring and evaluating Mississippi River water quality poses unique
challenges because (1) monitoring efforts face logistical difficulties and haz-
ards in some parts of the river system; (2) processes and natural fluctuations
in the Mississippi River operate on scales of decades and over hundreds of
miles; (3) the river spans, or forms, boundaries of political units or juris-
dictions that have differing priorities and resources; and (4) water quality
standards and environmental conditions vary across the entire system. For
example, because of natural, longitudinal changes in water quality from
upstream to downstream, levels of suspended sediment and turbidity that
would be considered “pristine” (i.e., pre-settlement) in the lower reaches
of the Mississippi River would be considered objectionable and indicative
of severe degradation if encountered in the river’s headwaters. Likewise,
because of natural patterns and differences along the river’s length, water

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
quality conditions (e.g., turbidity, temperature, dissolved oxygen) that ex-
ist in the headwaters can never be realized in the far downstream reaches.
Beyond typical longitudinal patterns, there are also large differences among
the subbasins within the Mississippi drainage basin. Any comprehensive
evaluation of Mississippi River water quality must consider these differences
along the river’s length and across the river’s watershed.
This chapter examines issues associated with evaluating Mississippi
River water quality. It describes some key features of the river and how its
hydrologic and watershed characteristics affect water quality monitoring.
The chapter reviews past and existing monitoring programs on the Mis-
sissippi River mainstem. It discusses the value of river system monitoring
in tracking changes in water quality and the importance of monitoring in
achieving Clean Water Act goals. It also discusses challenges of using data
and information from monitoring programs to help meet Clean Water Act
objectives. Finally, this chapter offers recommendations for enhanced state
and federal efforts to improve monitoring efficiency, reduce data gaps, and
strengthen implementation of the Clean Water Act.
MISSISSIPPI RIVER BASIN STRUCTURE,
HYDROLOGY, AND MONITORING
The mainstem Mississippi River exhibits markedly different hydrology,
sediment loads, and other features between its upstream and downstream
portions. These upstream-downstream differences are driven in large part
by inputs from the Mississippi’s two main tributaries, the Missouri and
Ohio Rivers, which enter the Mississippi at St. Louis, Missouri, and Cairo,
Illinois, respectively. The Missouri River is the longest tributary of the
Mississippi, and its flow is about two-thirds of the upper Mississippi River
above St. Louis. It carries a suspended sediment load several times that of
the upper Mississippi River (Meade, 1995). The dams constructed on the
Missouri River have reduced the Missouri’s total sediment contribution to
the Mississippi by more than half since 1953 (Meade and Parker, 1985;
Meade et al., 1990). As the Mississippi flows southward, the waters it re-
ceives from the Illinois and Missouri Rivers more than double its discharge
(Meade, 1995). Downstream, the Ohio River is the Mississippi’s largest
tributary with respect to discharge, carrying almost twice the discharge of
the upper Mississippi River above St. Louis (Table 2-1). Just as the river’s
discharge doubles when it receives the waters of the Missouri, its discharge
more than doubles again as it receives the waters of the Ohio River (Meade,
1995).
Downstream of the Mississippi River’s confluence with the Ohio River,
the river takes on a very different character than in its upstream reaches. In
the Mississippi’s lower reaches, the river becomes much deeper and wider

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0 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT
and in many areas contains swiftly moving, swirling, and turbulent water.
Author John Barry provides a colorful depiction of lower Mississippi River
hydraulics in his 1997 book, Rising Tide:
The complexity of the Mississippi exceeds that of nearly all other riv-
ers. Not only is it acted upon; it acts. It generates its own internal forces
through its size, its sediment load, its depth, variations in its bottom, its
ability to cave in the riverbank and slide sideways for miles, and even
tidal influences, which affect it as far north as Baton Rouge. Engineering
theories and techniques that apply to other rivers, even such major rivers
as the Po, the Rhine, the Missouri, and even the upper Mississippi, simply
do not work on the lower Mississippi, which normally runs far deeper and
carries far more water.
Monitoring efforts in the river’s lower stretches are difficult and hazardous
even under relatively calm conditions. These physical differences between
the upper and lower Mississippi River influence the ability of the states
along the river to monitor water quality and help explain some of the
differences in water quality monitoring efforts among the 10 Mississippi
River states.
Downstream of Cairo, the influence of direct lateral inputs (i.e., from
the adjoining bank or inflowing tributaries) to the Mississippi mainstem
becomes relatively less important. In the lower river, water quality thus
primarily is a function of upstream inputs, with less influence from the im-
mediately adjacent land. The states of the lower river thus understandably
consider the river’s condition, and possible water quality remedies, to be
largely beyond their control and responsibility. For example, the Mississippi
River and its basin upstream of Memphis, Tennessee, represent 80 percent
of the total drainage area, 76 percent of the total flow volume, and more
than 90 percent of the total riverbank miles for the entire system (Leopold
et al., 1964).
A consequence of the structure of the Mississippi River drainage sys-
tem is that the water quality in the mainstem of the lower river, because of
the large and relatively slowly changing mass of water involved, remains
relatively constant between those points at which major tributaries join
the flow. Thus, closely spaced sampling along the longitudinal axis of the
channel generally is not needed to get an accurate measure of average river
and water quality conditions over relatively large areas. However, because
inflowing tributaries may take many miles to mix completely with the main
body of the river, lateral and vertical patterns in water quality can be sub-
stantial and persistent. As the following sections explain, the influences of
the spatially variable Mississippi River drainage structure on water quality
have contributed to differences in U.S. federal and state monitoring of the
river and in how states along the river have approached Mississippi River
water quality monitoring.

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
FEDERAL AND REGIONAL MISSISSIPPI RIVER EVALUATIONS
As on many of the nation’s large rivers, various types of monitoring
have long been conducted on the Mississippi River. River flows have been
measured, water quality has been sampled, and ecosystem changes have
been tracked. The sum of these monitoring efforts presents a complex and
fragmented picture because they have been conducted by different federal
and state agencies and scientists, at differing spatial scales and time inter-
vals, with differing objectives, and with varied and changing budgets. Since
monitoring efforts are conducted at differing scales and for differing objec-
tives, there is no “one-size-fits-all” or standard river monitoring program.
Monitoring system designs and programs must consider and balance
a need for stability and continuity, on the one hand, with changes in sci-
entific paradigms, monitoring technologies and instrumentation, budgets,
and political and management objectives on the other. They must cope also
with the reality that it is not practical or feasible to monitor continuously
every site of interest in the system at hand (e.g., a large river) and that such
systems will always contain complexities and unknowns. Scientists must
gather and analyze enough information to improve scientific understand-
ing, while recognizing that there are limits to the amount of data that can
be gathered and there always will be some uncertainties regarding the state
and dynamics of large water systems or ecosystems. To help cope with these
realities, models of the system(s) being monitored are often developed so
data gathered from individual sites can be used to construct a quantitative
or conceptual framework of system-wide dynamics and behavior.
Federal Monitoring Programs
Federal agencies have sponsored and conducted the large-scale moni-
toring efforts for the Mississippi River. One of today’s prominent river mon-
itoring efforts is the Long Term Resource Monitoring Program (LTRMP).
Established in 1986 as part of the U.S. Army Corps of Engineers’ Envi-
ronmental Management Program (EMP) for the upper Mississippi River,
this initiative seeks to supply essential scientific information to the EMP
for the purposes of maintaining the upper Mississippi River as a viable
large river ecosystem with multiple uses (USGS, 1999). Since the LTRMP’s
inception, the Environmental Management Technical Center (EMTC) has
implemented the program. The EMTC today is part of the Upper Midwest
Environmental Sciences Center, which is a U.S. Geological Survey (USGS)
science center. The USGS, the U.S. Fish and Wildlife Service, and the five
upper Mississippi River basin states are cooperative partners in the EMP,
with the Corps of Engineers responsible for programmatic and financial
oversight. The LTRMP samples biota and water quality in five mainstem

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MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT
FIGURE 5-1 Long Term Resource Monitoring Program study areas (1993-2006).
SOURCE: USGS (1999).
Figure 5-1
reaches upstream of the Ohio River confluence to represent conditions and
habitat on the upper Mississippi River system (Figure 5-1). In each LTRMP
study reach, several hundred locations have been sampled for biota and
water quality since 1993 (Soballe and Fischer, 2004). The LTRMP-EMP is-
sued a comprehensive report in 1999 on upper Mississippi River ecological
status and trends. The report was described as “a milestone in the history of
the LTRMP. For the first time, data collected since the start of the LTRMP
are summarized in one report alongside historical observations and other
scientific findings” (USGS, 1999).

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
In addition to its efforts within the LTRMP, the USGS has been a leader
in other Mississippi River monitoring efforts, both in river flows and in
water quality sampling. USGS efforts in measuring discharge on the Mis-
sissippi River mainstem have remained relatively constant over the years,
but there has been a decrease in the extent of its water quality monitoring
efforts. For example, at its peak in the 1970s, the National Stream Quality
Accounting Network (NASQAN), operated by the USGS, provided exten-
sive coverage of the nation’s rivers, including the Mississippi. However, that
network has been steadily diminished in the number of sites, the number
of samples, and the number of parameters collected, and no other national
monitoring programs or monitoring by states and other entities has replaced
it. NASQAN data have been useful for several different applications and
computations. For example, USGS NASQAN data can be used to compute
long-term trends in the monthly nutrient flux at St. Francisville, Louisiana
(see Goolsby et al., 1999). Figure 5-2 shows changes in the number of active
FIGURE 5-2 History of active NASQAN sites at the national level. Reductions in
the network that were implemented in the late 1990s, and again in 2001, left only
four or five sites active on the Mississippi River mainstem (Clinton, Iowa; Grafton,
Ill.; Thebes, Ill.; and St. Francisville, Figure 5-2
La.).
SOURCE: Alexander et al. (1997).

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MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT
NASQAN sites from 1973 to 1995, and Figure 5-3 shows active NASQAN
sites across the United States as of 2000.
The USGS implemented the National Water Quality Assessment
(NAWQA) network in 1991, just as much of the NASQAN network was
being eliminated (USGS, 2007). However, the NAWQA program does
not represent a full replacement for NASQAN with regard to large riv-
ers. Although NAWQA includes many Mississippi River tributaries, it
includes no mainstem sites downstream of Lake Pepin. As a result, today
only a few mainstem water quality sites remain in the USGS network
downstream of Lake Pepin. These stations are at Clinton, Iowa; Grafton,
Illinois; Thebes, Illinois; and St. Francisville, Louisiana. The NASQAN
site on the Atchafalaya River at Melville, Louisiana, also could be in-
cluded in this group because the Atchafalaya is the Mississippi River’s
primary distributary in the Mississippi’s lower reaches (see Figure 5-3).
Although some monitoring sites have been lost, a monitoring station at
Belle Chasse, Louisiana, has come back online, and the USGS intends to
bring another Atchafalaya River station online. The loss of monitoring
sites of course represents the loss of future data from an individual site.
However, a greater concern with the loss of water quality monitoring sta-
FIGURE 5-3 Active NASQAN stations as of 2000.
SOURCE: USGS (2006).
Figure 5-3

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
tions is that large-scale assessments, which could be useful in addressing
regional or basinwide water management issues (e.g., hypoxia), cannot
be replicated because more recent data from the same area have not been
collected.
Comprehensive Mississippi River Assessments
Two widely cited water quality assessments that examine the Missis-
sippi River at a regional or system-wide scale were published in 1995 and
in 1999, and were headed by USGS scientists Robert Meade (1995) and
by Donald Goolsby (Goolsby et al., 1999), respectively (these two reports
are cited extensively in Chapter 2). In the 1995 report, the Meade team as-
sessed water quality conditions along the Mississippi River mainstem from
Minneapolis to New Orleans. They conducted longitudinal sampling on
seven dates from 1987 to 1990 between St. Louis and New Orleans and on
three additional dates from 1991 to 1992 between Minneapolis and New
Orleans. Results from the 1995 Meade study were used by the Goolsby
team as part of six reports that supported a Mississippi River assessment.
Although these two USGS studies are a rich source of data in terms of both
quality and quantity, they do not provide the coverage in space (many ar-
eas were unsampled) and time (these were snapshots or annual averages)
needed to detect the frequency and duration of water quality standard
violations for the Section 303(d) and Section 305(b) biennial assessments
of the river required by the Clean Water Act (CWA). Furthermore, it is
unlikely that these assessments can be repeated in the foreseeable future.
Similarly, the 1999 USGS status and trends report for the upper Missis-
sippi River, although a useful and creative synopsis of upper river ecology,
is not Clean Water Act specific. That is, it is not aimed at determining if
designated uses along the river are being met or assessing the frequency and
duration of violations of water quality standards.
There have been other assessments of water quality along select por-
tions of the river in addition to these studies. A 2002 report of water quality
changes and conditions in the upper river near the Twin Cities is an excel-
lent example (see Stoddard et al., 2002). However, no other studies have
attempted to evaluate and characterize the entire river like the reports from
the Meade and Goolsby teams.
The limited amount of water quality and river ecosystem data inhibits
evaluations of lower Mississippi River water quality. The USGS conducts
some sampling between Cairo and New Orleans, but this entails consider-
able difficulty, risk, and expense and therefore is very limited. Tennessee
has conducted only modest data collection efforts, most of which are from
the mainstem river directly downstream of Memphis. Arkansas, Kentucky,
and Mississippi generally conduct minimal or no water quality sampling

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MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT
in the Mississippi River mainstem. Louisiana State University and the
Louisiana Department of Environmental Quality have conducted more
Mississippi River water quality sampling and have compiled their results
into assessments.
There is a greater abundance of Mississippi River water quality data
for the upper Mississippi River than for the lower river, due in part to ef-
forts both of the federal-state EMP and LTRMP and of some upper river
states. Through its NASQAN and NAWQA programs, the USGS has col-
lected some water quality data for the Mississippi River, but these efforts
have not been systematic and sustained, they have not been directed toward
Clean Water Act objectives, and the resources allocated to these programs
generally have declined over time. As the following section explains, the
majority of water quality monitoring efforts along the Mississippi River
aimed specifically at Clean Water Act directives have been conducted at
the state level.
MONITORING ASSOCIATED WITH CLEAN
WATER ACT OBJECTIVES
Monitoring and other techniques that determine whether water qual-
ity standards are met, including water quality and designated uses, are key
steps toward achieving the Clean Water Act’s “fishable and swimmable”
objectives. Because states have the lead in implementing the Clean Water
Act, monitoring and the design of monitoring programs are state, not
federal, responsibilities. The Clean Water Act does not include any specific
monitoring requirements, such as frequency of monitoring, parameters to
be monitored, or locations for the siting of monitoring stations.
Water Quality Monitoring in an Interstate Setting
Several court decisions involving TMDL development have expressly
refused to require the U.S. Environmental Protection Agency (EPA) to con-
duct water quality monitoring (Sierra Club . Hankinson, 939 F. Supp. 865,
870 (N.D. Ga. 1996); Ala Center for the En’t . Reilly, 796 F. Supp. 1374,
1380 (W.D. Wash. 1992), aff’d 20 F.3d981, 987 (9th Cir. 1994)). Others
have found no legal mandate in the Clean Water Act for adequate state
monitoring prior to EPA action to approve or disapprove a list of impaired
waters that require TMDLs (Friends of the Wild Swan, Inc. . EPA, 130 F.
Supp. 2d 1184, 1193 (D. Mont. 1999); Sierra Club . EPA, 162 F. Supp. 2d
406, 413 n.5 and 416 (D. Md. 2001)). At the same time, however, Clean
Water Act Section 106(e)(1) conditions state receipt of federal grant funds
for water pollution control programs on the EPA’s finding that the state is
monitoring the quality of its surface waters and compiling and analyzing
the data obtained.

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
Water quality monitoring performed to meet Clean Water Act objec-
tives has some recognized deficiencies, and some reports have confirmed
the need to improve substantially the conduct of water quality monitoring,
in both quantity and quality, as an essential basis for credible water qual-
ity improvement programs (NACEPT, 1998; GAO, 2000a; NRC, 2001;
NAPA, 2002). For example, an EPA report commenting on state programs
noted (USEPA, 2003c):
States have taken very different approaches, within their resource limita-
tions, to implement their monitoring programs. They have applied a range
of monitoring and assessment approaches (e.g., water chemistry, sediment
chemistry, biological monitoring) to varying degrees, both spatially and
temporally, and at varying levels of sampling effort. It is not uncommon
for the reported quality of a water body (i.e. attainment or nonattainment)
to differ on either side of a state boundary. Although some differences
can be attributed to differences in water quality standards, variations in
data collection, assessment methods, and relative representativeness of the
available data contribute more to differences in assessment findings. These
differences adversely affect the credibility of environmental management
programs.
Moreover, the discipline and practice of water quality monitoring does not
always perfectly match CWA-related monitoring requirements. Water qual-
ity monitoring techniques and practices also are constantly being updated
and improved (see Box 5-1).
Interstate waters such as the Mississippi River pose significant problems
for the Clean Water Act framework. In addition to the size of such systems,
political boundaries can create jurisdictional complications and make it dif-
ficult for individual states to commit resources to water quality monitoring
in such waters. Moreover, given the Mississippi River’s interstate nature,
some states assume or assert that the monitoring and the condition of the
river are exclusively federal responsibilities. A statement in the Mississippi
Section 303(d) report for 2006 (MDEQ, 2006b) provides an example:
The Mississippi Department of Environmental Quality (MDEQ) is not
listing the Mississippi River on MDEQ’s Mississippi 2006 § 303(d) list. In
previous lists, the MDEQ included various segments of the river, but not
based on data. Because any TMDL or delisting decision deals with mul-
tiple states and multiple EPA Regions, the MDEQ considers this a national
issue. EPA Region 4 and Region 6 would jointly develop any TMDL for
the Mississippi River.
At the national level, the EPA compiles the Section 305(b) assessments
from each state into a national synthesis that is intended to indicate the con-
dition of the nation’s waters. In concept, at least, a similar approach could
be used to assess the entire Mississippi River. There are, however, shortcom-
ings with this approach, especially as it pertains to interstate rivers and to

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MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT
BOX 5-1
What Is Water Quality Assessment?
Under the Clean Water Act, water quality assessments are technical reviews of
physical-chemical, bacteriological, biological, and/or toxicological data and infor-
mation to determine the quality of a state’s surface water resources. Assessment
begins with the assignment of appropriate designated uses for waterbodies and
measurable water quality criteria that can be used to determine use attainment
(http://www.epa.gov/waterscience/standards/about/uses.htm). The criteria, which
may include biological, chemical, and physical measures, define the types of data
to be collected and assessed. The EPA Office of Water has developed national
indicators for surface waters and a conceptual framework for using environmen-
tal information in decision making (http://www.epa.gov/waterscience/standards
/about/crit.htm).
In the more traditional approach to water quality assessment, monitoring data
are compared to water quality criteria in order to make decisions on whether a
waterbody is supporting (or not) its designated uses, such as aquatic life support,
water contact recreation, and drinking water. This involves comparing criteria on
a parameter-by-parameter basis. Basic limitations of this approach are (1) mea-
surement of a set of individual physical, chemical, and biological parameters at
numerous points in an aquatic system is expensive; (2) measurements often are
available for only a few parameters; and (3) relating a set of parameter measure-
ments to the health of an aquatic system is often difficult.
A newer, faster, and less expensive water quality assessment approach, which
has emerged over the last two decades, is the use of rapid biological surveys,
or rapid bioassessment protocols (RBPs). This approach is a response, in part,
to dwindling resources available for monitoring efforts. It is also an attempt to
evaluate biological conditions rapidly and the effects of water quality on those
conditions in a particular system. In the RBP approach, surveys are conducted
of aquatic macroinvertebrates, fish, or periphyton, and the presence or absence
and relative abundance of species found is used to develop a numeric index that
can be compared to a rating scale. This approach requires calibration to specific
geographic area and, for the assessment of large rivers, is still in early stages of
development.
Whichever assessment approach is used, a determination is made of whether
the waterbody is fully supporting all of its uses; if not, the waterbody is consid-
ered impaired. The causes and sources of the impairment are then determined.
Impaired waters are subject to further monitoring and are listed on the state’s
Impaired Waters List. The EPA has national guidance on assessing and listing im-
paired waters, known as the Consolidated Assessment and Listing Methodology
(CALM), which generally undergoes revisions for each biennial reporting cycle.
an assessment at a regional or national scale. In particular, there is no sci-
entifically defensible (i.e., statistical) basis for combining and extrapolating
Section 305(b) assessments of individual waterbodies or reaches to make a
quantitative statement about the extent, frequency, or fraction of compli-
ance or noncompliance on a system-wide, regional, or national scale.

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MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT
BOX 5-2
Mississippi River Monitoring and Fish Consumption Advisories
A primary motivator of state-conducted monitoring of the Mississippi River is
the protection of fish resources and maintenance of up-to-date fish consumption
advisories. In fact, the issue of fish contamination is one of the greatest concerns
of sport and commercial fishermen and the general public along the upper Missis-
sippi River. Many commercial and recreational anglers depend heavily on Missis-
sippi River fishery resources, and many regional and local community economies
are supported by recreational use and river-related tourism.
Fisheries are jeopardized when toxins contaminate fish by direct exposure to
water or sediments or through the food chain. Some of these contaminants are
legacy materials (e.g., PCBs [polychlorinated biphenyls], DDT [dichlorodiphenyl-
trichloroethane]) and some derive from current practices (e.g., mercury, dioxin,
lead). These toxins can accumulate in fish tissue over time and reach concentra-
tions that pose a risk to human health. Concentrations of toxic substances in fish
tissue can be much higher than those found in the water.
States along the river monitor various fish species and use different ap-
proaches for assessing health risks. The states publish Fish Consumption Adviso-
ries (FCAs) that recommend limits on the consumption of fish, and they decide if
a river segment should be listed as impaired under the Clean Water Act because
of this contamination. Along some segments of the river, bordering states have
issued different FCAs and have categorized the impairment of the river section
differently. This can lead to public confusion about the risks from fish caught in
the river and can have economic and regulatory implications for point source dis-
chargers to the river (FTN Associates, Ltd. and Wenck Associates, Inc., 2005).
Evaluations of fish tissue quality differ from traditional water quality assess-
ment, which involves measurement of a particular water quality parameter and
comparing it to a criterion. Fish tissue analysis provides an aggregate measure
of aquatic organism exposure to a range of contaminants. Such analyses are
used in water quality impairment assessments and also support public health
protection through issuance of FCAs. The FCA process starts with collection and
analysis of fish tissue, proceeds to an evaluation of the risk to human health, and
then estimates what consumption limit (e.g., frequency and amount) should be
recommended for specific users (e.g., children, pregnant women) of specific fish
types (e.g., fish species, size, body portions) taken from specific areas. If fish
contaminants exceed a certain level or a FCA is issued for a waterbody, the river
segment may be added to the Clean Water Act Section 303(d) list of impaired
waterbodies.
The states, District of Columbia, U.S. territories, tribes, and local governments
have primary responsibilities for protecting their residents from the potential health
risks from eating contaminated fish caught in local waters. The states have de-
veloped their own fish advisory programs over the years, and there are variations
among them in terms of extent of monitoring, frequency of sampling, decisions
made regarding advisories, and so on. EPA plays a role in providing a National
Listing of Fish Advisories database. This is an annual compendium of information
on locally issued fish advisories and safe eating guidelines that is provided to
EPA by the states and other bodies. EPA has compiled and made this information
available since 1993 (available online at http://www.epa.gov/waterscience/fish/
advisories/2006/index.html#basic).

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
Mississippi River in its Section 305(b) assessments and Section 303(d) lists.
Differing combinations of data sources are used to evaluate each of Iowa’s
14 upper Mississippi River reaches (UMRBA, 2004).
With the possible exception of Louisiana, monitoring downstream of
the Ohio River confluence that is related to Clean Water Act assessment,
enforcement, and restoration is less active than in the upper Mississippi
River states. In general, the lower Mississippi River states consider Mis-
sissippi River water quality to be the responsibility of others and give it
low priority for monitoring funds. For example, Mississippi and Arkansas
provide an example of limited involvement in Mississippi River monitor-
ing, because they no longer assess the Mississippi mainstem as part of their
Section 305(b) process.
STATUS OF AND PROSPECTS FOR
MISSISSIPPI RIVER MONITORING
Current Efforts
The status of monitoring on the Mississippi River to obtain data rel-
evant to Clean Water Act assessment and enforcement presents a mixed
picture. Assessment of water quality and habitat for the Clean Water Act
has been done relatively well on the upper river, but even there, there are
limitations within the data gathered to date. Furthermore, levels of com-
mitment of the 10 Mississippi River states to river monitoring are varied
and may change in the future. Data collected often are not readily com-
parable (Box 5-3). Federal monitoring programs on the Mississippi River
are focused on fish and wildlife populations, habitat conditions, and mass
transport of nutrients and sediments. These programs are not designed to
be part of CWA-related monitoring (e.g., verifying whether a given state’s
designated uses are being attained).
The limitations of federal monitoring programs on the Mississippi
River are illustrated within the upper Mississippi River LTRMP. This pro-
gram has the primary purpose of monitoring biotic conditions and habitat
at a system-wide, multiyear scale. The water quality data collected by this
program are a primary source of information for substantial portions of the
upper river, and although it has been useful in Clean Water Act assessments
(e.g., by Minnesota), the LTRMP is focused on habitat conditions and is
not intended to track compliance with water quality standards. Thus, the
program does not monitor a host of pollutants that have numeric standards
and are priority pollutants of regulatory interest under the Clean Water Act,
nor does LTRMP monitoring lend itself to the detection of short-term, acute
conditions (e.g., violations of water quality standards) at specific locations
for specific durations or frequencies. Further, this program, like many other

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BOX 5-3
Consistency of Water Quality Data
The ability to combine or compare data from different sources is an important
issue with no easy solution. Data can differ not only because of differing methods
or equipment used to collect and analyze water samples, but also because of
differences in sampling design (i.e., what basic aspects of the system are repre-
sented in the data; see Soballe, 1998). For example, data that are collected during
midday sampling must be adjusted before they can be combined or compared
with data from a program that samples only at night or during pre-dawn hours.
Such an adjustment may not be possible. Likewise, data that are collected only
to represent high-flow storm conditions in one location may not be easily com-
bined or compared with data that sample end-of-pipe or low-flow conditions in
another. An approach often used in stream sampling programs is to collect a “flow-
weighted” sample in which a single sample is generated for chemical analysis by
adding water to a single container for several hours or several days in proportion
to the river’s surface elevation or flow. Such a sample is useful for calculating
mass transport, particularly during a single rainstorm or flood; however, results of
this flow integration are not readily comparable to those produced by sampling at
regular, longer-term intervals (weeks or months) to detect extremes or to estimate
average conditions. There is no single standard method that can be applied to all
sampling to meet all information needs.
federally sponsored efforts, has been reduced since the late 1990s and has
been forced to focus more closely on its primary mission of tracking the
status of biota and habitat in specific study areas. Although the LTRMP has
collected data from thousands of locations along the river for more than
15 years, these efforts have tended to be seasonal and limited to five river
reaches. There has been no mechanism to extrapolate these data to inter-
vening portions of the river or to other periods of time. Data collected by
the program clearly have value for improved understanding of Mississippi
River aquatic ecosystems (see, for example, USGS, 1999), but they have
limited utility regarding CWA-related assessment of the entire system.
The seemingly low level of Clean Water Act-related monitoring on por-
tions of the Mississippi River is not unique or even unusual. For example,
the GAO reported that as of 1996, states assessed only 19 percent of their
rivers and streams (GAO, 2000a). The GAO also noted that states tend
to focus monitoring on those waters with suspected pollution problems in
order to direct scarce resources to areas that could pose the greatest risk
(GAO, 2000a). Because of the dilution capacity of the Mississippi River,
the difficulty of large-river water quality monitoring, and the absence of

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
sole responsibility of individual states for its quality, states have given Mis-
sissippi River monitoring low priority.
A wide range of water quality and ecosystem monitoring efforts have
been and continue to be conducted along the Mississippi River. These ef-
forts are quite variable in spatial and temporal implementation, are not
well coordinated, and for the most part are not designed for Clean Water
Act assessment purposes. Better coordination and a shared sense of purpose
and value of monitoring information among the mainstem river states are
needed for more effective and useful system-wide monitoring.
The Value and Importance of Monitoring
Monitoring of Mississippi River water quality has not been performed
in a system-wide manner for extended periods (e.g., decades) and at inter-
vals of time (e.g., monthly) or space (in every major reach) that would sup-
port rigorous assessment of water quality and ecology for the river. As this
chapter has discussed, there are considerable challenges to conducting this
type of extensive monitoring: large-river sampling methods and instrumen-
tation need to be standardized; states and federal agencies must compare
and cooperate on sampling and monitoring strategies to make the most of
their expenditures and prevent duplication of ongoing efforts; the resources
required for extensive and sustained monitoring can be considerable; and
there are practical challenges to monitoring, especially in the often danger-
ous lower Mississippi River.
Despite the costs and analytical and logistical challenges involved in
creating such a program, there are also costs in not having a systematic
monitoring program for the entire Mississippi River and into the Gulf of
Mexico. The nation’s rivers, including the Mississippi, have realized im-
provements in some aspects of water quality as a result of the Clean Water
Act. Many of those improvements have been achieved through reductions
in point source discharges of pollutants.
Water quality issues and problems of primary concern along the river
today are different than in the early 1970s when the Clean Water Act was
enacted and consist primarily of nonpoint pollutant loads from agricultural,
urban, and suburban activities. The framework within the Clean Water Act
for addressing nonpoint source pollutants relies more strongly on scientific
data, monitoring, and modeling of water quality than on an end-of-pipe
approach to treating point source pollution (Box 5-4 discusses the role of
modeling in water quality assessments). Rather than focusing on reducing
discharge from individual sites, contemporary programs for achieving water
quality improvements in the Mississippi River and the Gulf of Mexico must
encompass pollutant inputs from across the entire watershed. They must
also monitor water quality conditions for the river as a whole, not just at

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MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT
BOX 5-4
Role of Modeling in Water Quality Assessment
Although acquisition and analysis of monitoring data is the approach preferred
by the EPA for identifying impaired waters, modeling can have an important
supplementary role. Integrated monitoring and modeling can often provide bet-
ter information than monitoring alone for the same total cost (NRC, 2001). For
example, Section 303(d) and related guidance from EPA recommend focusing
efforts on waterbodies or segments that are suspected of violating water quality
standards. Such targeted monitoring represents the use of available information
regarding water quality impairments to guide monitoring toward particular sites. A
potentially valuable use of modeling in relation to Section 303(d) listings would be
to formalize the use of available information on impairment probability in monitor-
ing system design. Limited monitoring resources could be focused on sites where
impairment is most uncertain, thus improving the efficiency of monitoring.
points near specific sources of effluent. Today, water quality improvements
rely more heavily on a science- and data-intensive approach to understand-
ing the linkages between activities that generate pollutant loads and their
ultimate impacts on waterbodies. Without comprehensive monitoring of a
river system, it is difficult to understand trends in water quality conditions,
to realize the impacts of watershed-focused programs designed to reduce
nutrient and sediment loads, and to determine whether designated uses are
being achieved.
Beyond limited amounts of data, another challenge to system-wide as-
sessment is that some of the data collected by the many state and federal
monitoring programs have fundamental differences in their underlying
purposes and designs (Box 5-4). When monitoring program details are
compared, it is often discovered that data from different sources cannot
be combined in a meaningful way. Thus, the ability to compare data over
large scales of time and space is further restricted. The situation is created,
in part, by the scales of time and space required for adequate research and
monitoring and by the specific issues the monitoring system is designed to
address. These scales are dictated by natural scales of the system and the
questions being addressed (Soballe, 1998), and the questions and issues
have seldom been the same across multiple monitoring programs.
For the Mississippi River, the lack of a coordinated water quality data
gathering program and of a centralized water quality information system
hinders effective implementation of the Clean Water Act and acts as a
barrier to maintaining or improving water quality along the river and in
the Gulf of Mexico. The EPA should take the lead in establishing such a
program. In doing so, it should work closely with the 10 Mississippi River

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
mainstem states and with federal agencies with relevant expertise and data,
such as the Corps of Engineers, the USGS, and the National Oceanic and
Atmospheric Administration (NOAA). Part of this effort should focus on
collecting data necessary to develop numeric water quality standards for
nutrients in the Mississippi River and the Gulf of Mexico.
Emerging Monitoring Challenges
Some emerging developments in aquatic system monitoring pose partic-
ular challenges for implementation in large systems such as the Mississippi
River. There is increasing interest in biological monitoring because of the
direct link to ecosystem health and the potential to evaluate the aggregate
impact of water pollution. Techniques and biocriteria have been developed
for smaller streams, but neither have been established yet for large rivers.
There also have been advances in tracking sources of sediment inputs to
streams.
Biomonitoring
In many Clean Water Act assessments, the condition of a waterbody
with respect to supporting a designated aquatic life use is evaluated pri-
marily through stream biological community assessments. Biomonitoring
of resident biota can often be conducted more quickly and less expensively
than monitoring of physical-chemical water quality parameters. Bioassess-
ment protocols (e.g., rapid bioassessment protocols; see Box 5-5) could fill
some data gaps with regard to the Mississippi River CWA-related assess-
ments, but this approach has been limited to date to wadable streams. In
addition, meaningful biocriteria (numeric measures of desirable fish popula-
tions, etc.) for large rivers have not been established, nor have means been
developed to readily collect the necessary data for sound bioassessments of
large rivers.
Impairments for human contact or consumption can also be assessed
using fish tissue analyses and evaluations of raw (intake) water monitored
by water purveyors. These are used in some reaches of the Mississippi
mainstem, but their application seems to be less than consistent (UMRBA,
2004). Recreational use impairments are often based on bacteriological
data, such as fecal coliform counts, and these are commonly used, at least
in the upper river.
Sediment Monitoring
Sediment concentration and transport are crucial water quality and river
ecology issues along the entire Mississippi River, but systematic monitoring

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0 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT
BOX 5-5
Rapid Bioassessment Protocols
Biological surveys and other direct measurements of the resident biota in sur-
face waters are often used to determine whether a surface waterbody is meeting
a designated aquatic life use. The Rapid Bioassessment Protocols (Barbour et
al., 1999) were developed in the 1980s and 1990s by various states and compiled
by the EPA in a guidance document. The guidance includes protocols for three
types of aquatic life—periphyton, benthic macroinvertebrates, and fish—as well
as for habitat assessment. These protocols have all been tested in streams and
wadable rivers in various parts of the United States. They have been used as
rapid, inexpensive means of water quality assessment and have been utilized
extensively by states in development of Section 305(b) water quality inventories.
Bioassessment has also been used in Section 303(d) impairment assessments.
Effects of excess nutrients, sediments, and other pollutant classes can be readily
identified.
Bioassessment protocols that are practicable and can be linked unequivocally
and quantitatively to the functional health (or biotic integrity) of the large river are
still under development. A limitation of the use of bioassessments for evaluating
conditions in large rivers such as the Mississippi River is the difficulty in linking
biological metrics unambiguously to specific causal factors. Thus, it currently is not
possible to initiate specific remedial action or management based on the numeri-
cal value of bioassessment indices alone. However, these indices can be valuable
for identifying the need for a more detailed evaluation of conditions in impaired
locations.
of these important variables poses analytical and conceptual challenges.
Standard, widely accepted approaches to assessing sediment dynamics (i.e.,
deposition and resuspension) have not been developed and accurate mea-
surements of sediment dynamics over long time periods (years) and large
spatial scales (tens to hundreds of kilometers) are difficult to obtain. For
example, reports on Mississippi River water quality and ecological integrity
often note sediment, “siltation,” and turbidity as priority concerns in the
upper river (UMRBA, 2004; Headwaters Group, 2005). These various terms
are interrelated and, although sometimes used interchangeably, do not have
the same meaning. Monitoring data for any one of these characteristics are
not particularly informative about the others. Turbidity, for example, is
governed by the size, composition, and concentration of suspended particles
in the water. It can be viewed as a short-term, near-field property because
the particles that create this phenomenon may change rapidly (minutes)
over short distances (meters) in the river. Monitoring that does not cap-
ture these short-term, near-field variations may not reveal the extremes of

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
turbidity to which river biota are exposed. Smaller particles (fine silts and
clays) have the greatest influence on turbidity, but coarser particles (sand)
usually dominate the process of sedimentation. In contrast to turbidity,
sedimentation is a longer-term processes (years to centuries), and assess-
ment of this phenomenon depends on the scales of space and time used in
the measurement. Moreover, the data used to study these processes on the
river generally are sparse (see Box 5-6).
As Figure 5-6 illustrates, an area that appears to be accumulating sedi-
ment for several years or decades may be deeply scoured by occasional large
floods and therefore be in dynamic balance over the longer term. Likewise,
one portion of a river reach may be accumulating sediment, while an adja-
cent zone is being scoured, so that on a larger spatial scale, the total reach
appears to be in balance. However, this balance may be only temporary and
extend over a few years or a few decades.
These complications and variations over time regarding sediment trans-
port and loadings are illustrative of the larger challenges that attend ac-
curate and consistent monitoring of water quality variables and provide
background for the following conclusions regarding federal and state water
quality monitoring programs along the Mississippi River.
BOX 5-6
Sediment Transport and Deposition: A Monitoring Challenge
A study of one of the upper Mississippi’s tributary streams—Coon Creek, in
Wisconsin—demonstrates some of the complex patterns of sediment transport
and deposition in a single stream, how those patterns may change over time (Fig-
ure 5-6), and the kind of monitoring needed to study long-term sediment transport
and deposition. Research in Coon Creek has shown that sediment yield varies
depending on where it is measured within a basin. Despite a significant decrease
of sediment flux within the basin caused by improved land management practices,
sediment yield from Coon Creek to the Mississippi River has held fairly constant
(at least according to available data). As indicated, this continued flow of sediment
is coming from upstream channels and banks.
There is presently only one sediment measuring station in this entire region
for tributaries to the Mississippi River. However, measurements on the main river
downstream at Dubuque, Iowa, indicate that sediment transport is presently only
about half the rate existing in the 1940s (Pannell, 1999). How can this apparent
disparity be explained? Are either or both measures wrong? There simply are not
enough sediment measuring stations to know.

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EVALUATING MISSISSIPPI RIVER WATER QUALITY
SUMMARY
Restoration and maintenance of water quality and related ecosystem
conditions in the Mississippi River require understanding of current system
conditions and trends over time. Monitoring data are necessary for the
assessment and planning required under the Clean Water Act to maintain
and improve water quality. However, large rivers such as the Mississippi
are difficult to monitor consistently and comprehensively for water quality
and biota. High-quality monitoring programs require expensive and rugged
equipment, specially trained personnel, and more time in the field than is
needed to monitor streams and small rivers. Further exacerbating the chal-
lenge of assessment of the Mississippi River is the fact that water quality
and habitat differ across the river’s many subbasins. Along the Mississippi
River, there are large longitudinal gradients in water quality, geomorphol-
ogy, and biota.
There is no consistency in the amount and quality of water quality data
available for the length of the mainstem Mississippi River. Some areas in the
upper river have been relatively well monitored and there is a large amount
of water quality data. At the federal level, these efforts primarily are rep-
resented by the EMP and LTRMP. Data from the LTRMP could be useful
in a supplementary role in Clean Water Act assessments, but the LTRMP
is focused on habitat conditions and is not intended to track compliance
with water quality regulations. The USGS also has collected some Missis-
sippi River water quality data via its NASQAN and NAWQA programs,
but these efforts have not been systematic and sustained, they have not been
directed toward Clean Water Act objectives, and the resources allocated to
the programs have generally declined over time.
On the upper river, Minnesota, Illinois, and Wisconsin have promoted
the most extensive Mississippi River programs at the state level, although
the resources devoted to these programs have varied over time. In the lower
river states, there are fewer data and there have been far fewer monitoring
initiatives. Tennessee has conducted only modest data collection efforts,
most of which are on the mainstem river directly downstream of Memphis.
Arkansas, Kentucky, and Mississippi generally conduct minimal or no wa-
ter quality sampling in the Mississippi River mainstem. Louisiana has con-
ducted more Mississippi River water quality sampling and has conducted
some assessments with the results. Some of these upstream-downstream
differences are driven by different values and uses of the respective portions
of the river; the physical difficulties and hazards posed by monitoring in the
large lower Mississippi River also are factors.
Water quality monitoring along the Mississippi River mainstem is in-
consistent over both space and time. The extent to which Mississippi River
mainstem states monitor water quality in the river varies considerably,

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MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT
and these efforts lack coordination. States along the river have assigned
different designated uses to the same river segments; they use different
judgments and methods in their assessments; and there is no standard for
the time frame or frequency of water quality monitoring. Mississippi River
monitoring programs conducted by the USGS and the Corps of Engineers
have diminished over time in many places, although the USGS is increas-
ing monitoring capabilities and the number of stations in some areas (e.g.,
Atchafalaya River). Generally speaking, the extent and quality of biologi-
cal, physical, and chemical data along the river generally do not support
thorough CWA-related assessments. The lack of a centralized Mississippi
River water quality information system and data gathering program hin-
ders effective application of the Clean Water Act and acts as a barrier to
maintaining and improving water quality along the Mississippi River and
into the northern Gulf of Mexico.
States along the mainstem Mississippi River, together with the federal
government, need to coordinate better with respect to planning monitoring
activities and sharing the data that result. In a climate of ever-decreasing
resources for monitoring, all federal and state agencies involved in moni-
toring the Mississippi River mainstem should cooperate and coordinate
their efforts to the greatest extent possible. The Mississippi River clearly is
of federal interest because of the many states in the river basin, the river’s
prominent role in supporting interstate commerce, and its hydrologic and
ecological systems that extend across several states and into the Gulf of
Mexico. The federal government should take the lead in ensuring adequate
water quality monitoring, a cornerstone of effective Clean Water Act imple-
mentation along the Mississippi River and into the Gulf of Mexico.
There is a clear need for federal leadership in system-wide monitoring
of the Mississippi River. The EPA should take the lead in establishing a
water quality data sharing system for the length of the Mississippi River.
This would include establishing coordinated monitoring designs and de-
veloping mechanisms (hardware, software, and protocols) necessary for
efficient data sharing among monitoring and resource agencies and Section
305(b) and Section 303(d) assessment teams. It also would entail ensuring
consistency in river monitoring in terms of parameters measured, units and
methods employed, and siting of monitoring stations along the length of
the river. The EPA should draw on the considerable expertise and data held
by the U.S. Army Corps of Engineers and the USGS, as well as NOAA and
the water-related data for the northern Gulf of Mexico that it collects and
maintains. The EPA should work closely with Mississippi River states in
establishing this plan and system. A priority for EPA in this regard should
be to coordinate with the states to ensure the collection of data necessary
to develop numeric water quality standards for nutrients in the Mississippi
River and the Gulf of Mexico.